From d3dbb074fd8e9b89795ce2d42f5a72919b74cf27 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 26 Apr 2024 10:15:35 +0200 Subject: [PATCH 1/3] feat(modules_testdata_base_path): update guidelines for test data --- src/content/docs/contributing/test_data_guidelines.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/content/docs/contributing/test_data_guidelines.md b/src/content/docs/contributing/test_data_guidelines.md index cc022c20a3..592753c1c8 100644 --- a/src/content/docs/contributing/test_data_guidelines.md +++ b/src/content/docs/contributing/test_data_guidelines.md @@ -57,10 +57,9 @@ In contrast, if your module requires many tests, steps, or heavy CPU usage, you 11. The test data pull request requires a review to be merged. -12. Once you've had your pull request merged in into `nf-core/test-datasets`, make another PR into [nf-core/modules](https://github.com/nf-core/modules), to add your file as a new entry to the [`modules/tests/config/test_data.config`](https://github.com/nf-core/modules/blob/master/tests/config/test_data.config). +12. Once you've had your pull request merged in into `nf-core/test-datasets`, you are good to go and you can use the newly created file(s) for your test. Use `params.modules_testdata_base_path` to point to the test data directory in your module, and append to it the path to the file(s) you need. This is an example using the `fasta` file from `sarscov2`: - - This only applies field-specific collections, `delete_me/` files are excluded from this, and raw github URLs should be used in tests. - - The 'key' for each URL should follow the style of the full file name with extensions but with underscores rather than full-stops e.g. `genome.fa.gz` would become `genome_fa_gz`. + - `file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)` ### Field specific guidance From 9af2d0d9faef223d4cd2daa0972475eb9a865a7b Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 26 Apr 2024 10:44:26 +0200 Subject: [PATCH 2/3] Apply suggestions from code review Co-authored-by: James A. Fellows Yates --- src/content/docs/contributing/test_data_guidelines.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/content/docs/contributing/test_data_guidelines.md b/src/content/docs/contributing/test_data_guidelines.md index 592753c1c8..5e47cf6d06 100644 --- a/src/content/docs/contributing/test_data_guidelines.md +++ b/src/content/docs/contributing/test_data_guidelines.md @@ -57,9 +57,10 @@ In contrast, if your module requires many tests, steps, or heavy CPU usage, you 11. The test data pull request requires a review to be merged. -12. Once you've had your pull request merged in into `nf-core/test-datasets`, you are good to go and you can use the newly created file(s) for your test. Use `params.modules_testdata_base_path` to point to the test data directory in your module, and append to it the path to the file(s) you need. This is an example using the `fasta` file from `sarscov2`: +12. Once you've had your pull request merged in into `nf-core/test-datasets`, you are good to go and you can use refer to the newly uploaded file(s) for your tests. Use `params.modules_testdata_base_path` to point to the test data directory in your module, and append to it the path to the file(s) you need. an example using the `fasta` file from `sarscov2`: - `file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)` + - Note the file string corresponds to the directory structure of the modules repository. ### Field specific guidance From 907adc003bffcf930e796d5c6a0763187f0c5c7c Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 26 Apr 2024 10:45:04 +0200 Subject: [PATCH 3/3] Apply suggestions from code review --- src/content/docs/contributing/test_data_guidelines.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/content/docs/contributing/test_data_guidelines.md b/src/content/docs/contributing/test_data_guidelines.md index 5e47cf6d06..2c3ab6dcdd 100644 --- a/src/content/docs/contributing/test_data_guidelines.md +++ b/src/content/docs/contributing/test_data_guidelines.md @@ -57,7 +57,7 @@ In contrast, if your module requires many tests, steps, or heavy CPU usage, you 11. The test data pull request requires a review to be merged. -12. Once you've had your pull request merged in into `nf-core/test-datasets`, you are good to go and you can use refer to the newly uploaded file(s) for your tests. Use `params.modules_testdata_base_path` to point to the test data directory in your module, and append to it the path to the file(s) you need. an example using the `fasta` file from `sarscov2`: +12. Once you've had your pull request merged in into `nf-core/test-datasets`, you are good to go and you can use refer to the newly uploaded file(s) for your test(s). Use `params.modules_testdata_base_path` to point to the test data directory in your module, and append to it the path to the file(s) you need. an example using the `fasta` file from `sarscov2`: - `file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)` - Note the file string corresponds to the directory structure of the modules repository.